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FEBS Journal

Cover image for Vol. 281 Issue 1

January 2014

Volume 281, Issue 1

Pages i–iii, 1–432

  1. Front Cover

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Editor's Choice
    6. Review Articles
    7. Original Articles
    8. Author index
    9. Table of Contents
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      Front Cover (page i)

      Article first published online: 2 JAN 2014 | DOI: 10.1111/febs.12627

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      L1 retrotransposition and silencing pathway by P.E. Carreira et al. (pp. 63–73).

  2. Editorial Information

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Editor's Choice
    6. Review Articles
    7. Original Articles
    8. Author index
    9. Table of Contents
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      Editorial Information (pages ii–iii)

      Article first published online: 2 JAN 2014 | DOI: 10.1111/febs.12627_1

  3. Editorial

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Editor's Choice
    6. Review Articles
    7. Original Articles
    8. Author index
    9. Table of Contents
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      The FEBS Journal: passing the editorial baton (pages 1–2)

      Seamus J. Martin

      Article first published online: 19 DEC 2013 | DOI: 10.1111/febs.12650

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      Seamus Martin, the new Editor-in-Chief of FEBS Journal, outlines his plans for the journal and pays tribute to his predecessor Richard Perham.

  4. Editor's Choice

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Editor's Choice
    6. Review Articles
    7. Original Articles
    8. Author index
    9. Table of Contents
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      Leucine-rich repeat kinase 2 regulates tau phosphorylation through direct activation of glycogen synthase kinase-3β (pages 3–13)

      Fumitaka Kawakami, Naoki Shimada, Etsuro Ohta, Go Kagiya, Rei Kawashima, Tatsunori Maekawa, Hiroko Maruyama and Takafumi Ichikawa

      Article first published online: 28 NOV 2013 | DOI: 10.1111/febs.12579

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      Leucine-rich repeat kinase 2 (LRRK2) is one of the most important genetic factors influencing the risk of developing Parkinson's disease, but despite 10 years of research we do not have a clear idea as to how LRRK2 influences pathology. In this issue, Kawakami and coworkers provide evidence that LRRK2 can regulate the activity of GSK-3β, a kinase that regulates the phosphorylation of Tau, a central player in neurodegeneration and a protein that is deposited in the brains of some individuals with mutations in LRRK2. Perhaps this is part of the missing link.

  5. Review Articles

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Editor's Choice
    6. Review Articles
    7. Original Articles
    8. Author index
    9. Table of Contents
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      The enzymes of human diphosphoinositol polyphosphate metabolism (pages 14–33)

      Mark P. Thomas and Barry V. L. Potter

      Article first published online: 5 NOV 2013 | DOI: 10.1111/febs.12575

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      This review covers the three classes of enzymes involved in the metabolism of diphosphoinositol polyphosphates – inositol hexakisphosphate kinases (IP6K), inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinases (PPIP5K), and diphosphoinositol polyphosphate phosphohydrolases (DIPP). It looks at both the catalytic and non-catalytic roles of these enzymes and their effects on pathway and cellular function.

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      Emerging trends of long non-coding RNAs in gene activation (pages 34–45)

      Jaya Krishnan and Rakesh K. Mishra

      Article first published online: 13 NOV 2013 | DOI: 10.1111/febs.12578

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      The central dogma of biology is due for new dimensions with the emergence of numerous non-coding RNAs (ncRNAs) as the final functional product. Until recently, most of the ncRNAs were known to have repressive function. Here we discuss the gene activation role of long ncRNAs that form a significant proportion of these transcripts, which also reveals their functional versatility.

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      The role of protein glycosylation in Alzheimer disease (pages 46–62)

      Sophia Schedin-Weiss, Bengt Winblad and Lars O. Tjernberg

      Article first published online: 26 NOV 2013 | DOI: 10.1111/febs.12590

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      This review summarizes the current knowledge on the roles of protein glycosylation in Alzheimer Disease (AD). Defects in glycosylation of two proteins of major importance in AD, Tau and the amyloid precursor protein (APP), as well as other proteins, have been reported in AD. These findings indicate that protein glycosylation is of importance in AD pathogenesis.

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      L1 retrotransposons, cancer stem cells and oncogenesis (pages 63–73)

      Patricia E. Carreira, Sandra R. Richardson and Geoffrey J. Faulkner

      Article first published online: 28 NOV 2013 | DOI: 10.1111/febs.12601

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      LINE-1 (L1) retrotransposition is a source of ongoing genetic variation within and between human populations. Somatic L1 mobilisation has also recently been reported in cancer and may, in some cases, contribute to tumorigenesis. Here we discuss how L1 retrotransposition could trigger neoplastic transformation, based on the observed relationships between cellular plasticity, L1-mediated insertional mutagenesis and altered gene expression.

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      Protein universe containing a PUA RNA-binding domain (pages 74–87)

      Carolina S. Cerrudo, Pablo D. Ghiringhelli and Daniel E. Gomez

      Article first published online: 28 NOV 2013 | DOI: 10.1111/febs.12602

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      Review of the current knowledge about PUA domain containing proteins, in order to illustrate the progress in this field. We presented an update of proteins having this domain, focusing on specific proteins which are present in Homo sapiens and exploring the existence of these in other species, analyzing also the phylogenetic distribution of PUA domain in different species and proteins.

  6. Original Articles

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Editor's Choice
    6. Review Articles
    7. Original Articles
    8. Author index
    9. Table of Contents
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      Curcumin up-regulates phosphatase and tensin homologue deleted on chromosome 10 through microRNA-mediated control of DNA methylation – a novel mechanism suppressing liver fibrosis (pages 88–103)

      Jianjian Zheng, Cunzao Wu, Zhuo Lin, Yong Guo, Liang Shi, Peihong Dong, Zhongqiu Lu, Shenmeng Gao, Yi Liao, Bicheng Chen and Fujun Yu

      Article first published online: 5 NOV 2013 | DOI: 10.1111/febs.12574

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      We report that the methylation of PTEN was reduced by curcumin via miR-29b and DNMT3b, and DNMT3b is one of the genes targeted by miR-29b in rat. It was further confirmed that curcumin-mediated PTEN up-regulation, DNMT3b down-regulation, and PTEN hypomethylation were all attenuated by miR-29b inhibitor. Therefore, miRNA-mediated epigenetic regulation may be a novel mechanism suppressing liver fibrosis.

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      Monitoring gene expression in a single Xenopus oocyte using multiple cytoplasmic collections and quantitative RT-PCR (pages 104–114)

      Alexander A. Tokmakov, Takanori Hashimoto, Yushi Hasegawa, Sho Iguchi, Tetsushi Iwasaki and Yasuo Fukami

      Article first published online: 13 NOV 2013 | DOI: 10.1111/febs.12576

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      We describe a simple and reliable technique for monitoring gene expression in a single living Xenopus oocyte. It is based on multiple collections of nanoliter amounts of the oocyte cytoplasm and qRT-PCR. The technique allows monitoring expression dynamics of heterologous genes and profiling of multiple endogenous transcripts in the single oocyte. It exerts minimal effect on oocyte viability.

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      Up-regulation of survivin by AKT and hypoxia-inducible factor 1α contributes to cisplatin resistance in gastric cancer (pages 115–128)

      Xue-Pu Sun, Xuesong Dong, Lele Lin, Xian Jiang, Zheng Wei, Bo Zhai, Bo Sun, Qiang Zhang, Xiaolong Wang, Hongchi Jiang, Geoffrey W. Krissansen, Haiquan Qiao and Xueying Sun

      Article first published online: 18 NOV 2013 | DOI: 10.1111/febs.12577

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      Survivin is associated with resistance to chemotherapy in gastric cancer. Here, we demonstrate that upregulation of survivin by AKT and hypoxia-inducible factor (HIF)-1α contributes to the resistance of gastric cancer cells to cisplatin (CDDP). The results indicate that inhibition of these pathways may be a potential strategy for overcoming CDDP resistance in the treatment of gastric cancer.

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      On the catalytic mechanism and stereospecificity of Escherichia coli l-threonine aldolase (pages 129–145)

      Martino L. di Salvo, Soumya G. Remesh, Mirella Vivoli, Mohini S. Ghatge, Alessandro Paiardini, Simona D'Aguanno, Martin K. Safo and Roberto Contestabile

      Article first published online: 13 NOV 2013 | DOI: 10.1111/febs.12581

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      l-Threonine aldolases are enzymes whose biological function is unclear but are biotechnologically relevant for bioorganic synthesis of l-3-hydroxyamino acids. Our structural and functional characterization of the Escherichia coli enzyme suggests that stereospecificity is determined by the overall microenvironment of the active site. A structural water molecule has been proposed to act as catalytic base in the retro-aldol cleavage reaction.

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      3′–UTR-dependent regulation of mRNA turnover is critical for differential distribution patterns of cyclic gene mRNAs (pages 146–156)

      Yasuhide Nitanda, Takaaki Matsui, Tatsuro Matta, Aya Higami, Kenji Kohno, Yasukazu Nakahata and Yasumasa Bessho

      Article first published online: 18 NOV 2013 | DOI: 10.1111/febs.12582

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      In mouse development, Lunatic fringe (Lfng) and Hes7 show oscillatory expression in the presomitic mesoderm, thereby controlling cyclic somite formation. They receive a common transcriptional regulation, but their mRNA distribution patterns are different. We demonstrate that 3′UTR-dependent rapid turnover of Lfng and Hes7 plays a critical role in their dynamic expression patterns using transgenic mice with their 3′UTR.

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      T-cell immunoglobulin and mucin domain 2 (TIM-2) is a target of ADAM10-mediated ectodomain shedding (pages 157–174)

      Christin Dewitz, Katja Möller-Hackbarth, Olga Schweigert, Karina Reiss, Athena Chalaris, Jürgen Scheller and Stefan Rose-John

      Article first published online: 19 NOV 2013 | DOI: 10.1111/febs.12583

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      T-cell immunoglobulin and mucin domain 2 (TIM-2) is expressed on activated B cells. TIM-2 is a target of A Disintegrin and Metalloprotease (ADAM)10-mediated ectodomain shedding resulting in the generation of a soluble form of TIM-2. TIM-2 shedding was negatively controlled by calmodulin. Soluble TIM-2 interacted with H-ferritin. Shedding of TIM-2 revealed the involvement of ADAM proteases in cellular iron-homeostasis.

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      The COP9 signalosome is involved in the regulation of lipid metabolism and of transition metals uptake in Saccharomyces cerevisiae (pages 175–190)

      Valerio Licursi, Chiara Salvi, Virginia De Cesare, Teresa Rinaldi, Benedetta Mattei, Claudia Fabbri, Giovanna Serino, Laylan Bramasole, Jacob Z. Zimbler, Elah Pick, Brett M. Barnes, Martin Bard and Rodolfo Negri

      Article first published online: 25 NOV 2013 | DOI: 10.1111/febs.12584

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      The COP9 signalosome (CSN) is a highly conserved eukaryotic protein complex which regulates the Cullin-RING family of ubiquitin ligases. We conducted a transcriptomic, proteomic and phenotypical analysis of a S. cerevisiae strain deleted in the CSN5/RRI1 catalytic subunit, which shows that CSN is involved in the regulation of genes controlling amino acid and lipid metabolism, and transition metals uptake.

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      Nucleic acid delivery by cell penetrating peptides derived from dengue virus capsid protein: design and mechanism of action (pages 191–215)

      João M. Freire, Ana Salomé Veiga, Inês Rego de Figueiredo, Beatriz G. de la Torre, Nuno C. Santos, David Andreu, Andrea T. Da Poian and Miguel A. R. B. Castanho

      Article first published online: 28 NOV 2013 | DOI: 10.1111/febs.12587

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      Two peptides, pepM and pepR, designed from two domains of the dengue virus capsid protein, were studied as cell penetrating peptides (CPPs). Studies performed by confocal microscopy and flow cytometry showed that pepM translocates lipid membranes directly, while pepR requires endocytosis. The translocation kinetics of both peptides was monitored by real-time flow cytometry.

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      Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1 (pages 216–231)

      Chiara Zucchelli, Simone Tamburri, Giacomo Quilici, Eleonora Palagano, Andrea Berardi, Mario Saare, Pärt Peterson, Angela Bachi and Giovanna Musco

      Article first published online: 25 NOV 2013 | DOI: 10.1111/febs.12588

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      Sp140-PHD solution structure shows prolyl isomerization in the L3 loop and presents an atypical PHD finger fold which does not bind to histone H3 tails, but is recognized by Pin1. Pin1 specifically binds to a phosphopeptide corresponding to the L3 loop of Sp140-PHD and catalyzes cis-trans isomerization of a pThr-Pro bond. Co-immunoprecipitation experiments demonstrate FLAG-Sp140 interaction with Pin1 in vivo.

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      pH-Dependent hydrolase, glutaminase, transpeptidase and autotranspeptidase activities of Bacillus subtilis γ-glutamyltransferase (pages 232–245)

      Carlo F. Morelli, Cinzia Calvio, Marco Biagiotti and Giovanna Speranza

      Article first published online: 26 NOV 2013 | DOI: 10.1111/febs.12591

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      B. subtilis γ-glutamyltransferase (γ-GT) catalyzes the transfer of the γ-glutamyl moiety from glutamine to an acceptor amino acid. Representative γ-GT-catalyzed reactions are presented and detailed analyses of the reaction products are given. We found that hydrolase, transpeptidase and autotranspeptidase activities are strongly modulated by the pH of the reaction medium, that influences the protonation state of the acceptor substrates.

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      Characterization of a periplasmic nitrate reductase in complex with its biosynthetic chaperone (pages 246–260)

      Jennifer M. Dow, Sabine Grahl, Richard Ward, Rachael Evans, Olwyn Byron, David G. Norman, Tracy Palmer and Frank Sargent

      Article first published online: 9 DEC 2013 | DOI: 10.1111/febs.12592

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      The bacterial periplasmic nitrate reductase, NapA, is bound tightly during its biosynthesis by the NapD chaperone. Here, pulsed EPR, analytical ultracentrifugation, and small angle X-ray scattering were used to characterise the complex. This work indicates that the NapD chaperone binds primarily at the NapA signal peptide, and the proteins are present in the NapDA complex in a 1 : 1 molar ratio.

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      GTP binding controls complex formation by the human ROCO protein MASL1 (pages 261–274)

      Sybille Dihanich, Laura Civiero, Claudia Manzoni, Adamantios Mamais, Rina Bandopadhyay, Elisa Greggio and Patrick A. Lewis

      Article first published online: 28 NOV 2013 | DOI: 10.1111/febs.12593

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      MASL1 is a member of the ROCO family of proteins, characterised by a Ras of complex proteins/GTPase domain. In this study, we investigated the biochemical properties of MASL1 and the relationship between guanosine nucleotide binding and complex formation. During our investigations we identified HSP60 as a binding partner for MASl1.

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      Surface structural dynamics of enzymatic cellulose degradation, revealed by combined kinetic and atomic force microscopy studies (pages 275–290)

      Manuel Eibinger, Patricia Bubner, Thomas Ganner, Harald Plank and Bernd Nidetzky

      Article first published online: 10 DEC 2013 | DOI: 10.1111/febs.12594

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      Surface dynamic processes involved in enzymatic degradation of a mixed amorphous-crystalline cellulosic model substrate (MACS) were characterized using in situ visualization by atomic force microscopy combined with kinetic studies. Three-dimensional surface degradation by cellulases resulted in increased enzyme adsorption. The specific activity of adsorbed cellulases declined nonetheless as cellulose conversion progressed, reflecting increasingly nonproductive interaction between enzymes and the substrate surface.

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      Structure and expression profile of the sucrose synthase gene family in the rubber tree: indicative of roles in stress response and sucrose utilization in the laticifers (pages 291–305)

      Xiaohu Xiao, Chaorong Tang, Yongjun Fang, Meng Yang, Binhui Zhou, Jiyan Qi and Yi Zhang

      Article first published online: 26 NOV 2013 | DOI: 10.1111/febs.12595

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      Six sucrose synthase (Sus) genes were first identified and characterized in Hevea brasiliensis, which comprise the entire gene family in this tree species. The results give a new insight into the structure and expression profile of the Hevea Sus family, with a potential role in both stress responses and the regulation of sucrose utilization in the rubber- producing cells-laticifers.

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      Large-scale analysis of somatic hypermutations in antibodies reveals which structural regions, positions and amino acids are modified to improve affinity (pages 306–319)

      Anat Burkovitz, Inbal Sela-Culang and Yanay Ofran

      Article first published online: 26 NOV 2013 | DOI: 10.1111/febs.12597

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      A large-scale structural analysis of antibodies somatic hypermutations (SMHs) reveals the principles that guide affinity maturation. AID hotspots, previously believed to play a key role in guiding SMHs, are not a major driving force in determining the sequence of the mature antibody. The effect on binding energy is a key factor in directing SHMs in all parts of the antibody.

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      Improved asymmetry prediction for short interfering RNAs (pages 320–330)

      Amanda P. Malefyt, Ming Wu, Daniel B. Vocelle, Sean J. Kappes, Stephen D. Lindeman, Christina Chan and S. Patrick Walton

      Article first published online: 2 JAN 2014 | DOI: 10.1111/febs.12599

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      Identifying highly active siRNAs is important for developing RNA interference therapeutics. Here, we describe an algorithm for predicting highly active siRNA sequences based solely on two asymmetry parameters, end sequence nucleotides and thermodynamic stabilities. Use of these parameters combined improves the prediction of siRNA activity over current asymmetry approaches when tested on enhanced green fluorescent protein and protein kinase R.

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      Structural analysis of Mycobacterium tuberculosis ATP-binding cassette transporter subunit UgpB reveals specificity for glycerophosphocholine (pages 331–341)

      Dunquan Jiang, Qingqing Zhang, Qianqian Zheng, Hao Zhou, Jin Jin, Weihong Zhou, Mark Bartlam and Zihe Rao

      Article first published online: 2 DEC 2013 | DOI: 10.1111/febs.12600

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      Nutritional requirements for Mycobacterium tuberculosis growth and the corresponding transporters remain unknown. We determined the 1.5-Å crystal structure of M. tuberculosis UgpB, an ABC transporter subunit. Structural and biochemical analysis shows it does not bind sn-glycerol-3-phosphate as predicted, but instead binds glycerophosphocholine. Elucidating the carbon and phosphate source for M. tuberculosis inside the host should lead to improved anti-tuberculosis therapeutics.

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      Temperature effects on the fidelity of a thermostable HIV-1 reverse transcriptase (pages 342–351)

      Mar Álvarez and Luis Menéndez-Arias

      Article first published online: 26 NOV 2013 | DOI: 10.1111/febs.12605

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      Little is known on the effect of the temperature on the accuracy of reverse transcriptases (RTs), since fidelity estimates have been usually obtained at 37 °C. At 50–55 °C, wild-type HIV-1 group O RT (a thermostable polymerase) shows error rates of (1.3–2.8) × 10−5, lower than those obtained at 37 °C and similar to the values reported for the most faithful retroviral RTs.

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      Localization of SERBP1 in stress granules and nucleoli (pages 352–364)

      Yu-Jen Lee, Hung-Ming Wei, Ling-Yun Chen and Chuan Li

      Article first published online: 9 DEC 2013 | DOI: 10.1111/febs.12606

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      SERBP1 (SERPINE1 mRNA binding protein 1) is an arginine methylated RNA binding protein and the modification affects its protein interaction and intracellular localization. We show that after arsenite treatment, a fraction of SERBP1co-localizes with the stress granule (SG) marker TIA-1in the cytoplasmic SGs. Besides, upon arsenite treatment, diffuse cytoplasmic localization of SERBP1 shifts to nuclear-dominant and concentrated nucleolar distribution.

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      Periplasmic glucose-binding protein from Pseudomonas putida CSV86 – identification of the glucose-binding pocket by homology-model-guided site-specific mutagenesis (pages 365–375)

      Arnab Modak, Prasenjit Bhaumik and Prashant S. Phale

      Article first published online: 9 DEC 2013 | DOI: 10.1111/febs.12607

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      Glucose transport in Pseudomonas putida CSV86 is mediated via a substrate-specific periplasmic glucose-binding protein (ppGBP). The homology model of ppGBP showed highest structural similarity with GBP of Thermus thermophilus. Alanine substitution of residues forming putative glucose binding pocket of ppGBP resulted in the significant loss of glucose binding activity thus highlighting the significance of these residues.

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      Evaluation of all non-synonymous single nucleotide polymorphisms (SNPs) in the genes encoding human deoxyribonuclease I and I-like 3 as a functional SNP potentially implicated in autoimmunity (pages 376–390)

      Misuzu Ueki, Kaori Kimura-Kataoka, Haruo Takeshita, Junko Fujihara, Reiko Iida, Rie Sano, Tamiko Nakajima, Yoshihiko Kominato, Yasuyuki Kawai and Toshihiro Yasuda

      Article first published online: 10 DEC 2013 | DOI: 10.1111/febs.12608

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      We have evaluated all of the 44 and 25 non-synonymous SNPs in the human DNase 1 and I-like 3 genes, respectively, potentially implicated in autoimmune diseases, as a functional SNP. A minor allele of 13 SNPs producing a loss-of-function variant in both the DNase genes, irrespective of extremely low genetic heterogeneity, would be a direct genetic risk factor for autoimmune diseases.

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      The specificity and kinetic mechanism of branched-chain amino acid aminotransferase from Escherichia coli studied with a new improved coupled assay procedure and the enzyme's potential for biocatalysis (pages 391–400)

      Xuejing Yu, Xingguo Wang and Paul C. Engel

      Article first published online: 9 DEC 2013 | DOI: 10.1111/febs.12609

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      E.coli branched-chain amino acid aminotransferase, studied with (R)-hydroxyglutarate dehydrogenase for coupling, gave reliable kinetic constants for asymmetric synthesis of amino acids including non-natural l-norleucine, l-norvaline and l-neopentylglycine. Kinetic results are compared with molecular modelling. A two-substrate study for several substrates indicates ping-pong kinetics. For good 2-oxoacid substrates, 2-oxoglutarate release is rate-limiting during transamination reaction under conditions of substrate saturation.

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      A novel class of bifunctional acylpeptide hydrolases – potential role in the antioxidant defense systems of the Antarctic fish Trematomus bernacchii (pages 401–415)

      Marta Gogliettino, Alessia Riccio, Marco Balestrieri, Ennio Cocca, Angelo Facchiano, Teresa M. D'Arco, Clara Tesoro, Mosè Rossi and Gianna Palmieri

      Article first published online: 10 DEC 2013 | DOI: 10.1111/febs.12610

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      Oxidative challenge is an important factor affecting the adaptive strategies of Antarctic fish. This study represents the first report on piscine APEHs specifically from the Antarctic teleost Trematomus bernacchii. Two apeh cDNAs were isolated and the encoded proteins (APEH1Tb/APEH-2Tb) appeared to belong to different phylogenetic clusters and displayed distinct molecular-functional behaviors revealing an unusual activity of APEH-2Tb towards oxidized proteins.

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      Structure-based analysis of thermodynamic and mechanical properties of cavity-containing proteins – case study of plant pathogenesis-related proteins of class 10 (pages 416–429)

      Mateusz Chwastyk, Mariusz Jaskolski and Marek Cieplak

      Article first published online: 2 DEC 2013 | DOI: 10.1111/febs.12611

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      We provide theoretical comparisons of the physical properties of eighteen proteins with the PR-10 fold, which is characterized by a large hydrophobic cavity. Our novel algorithm to calculate the volume of internal cavities within protein structures is used to demonstrate that although the sizes of the cavities of the investigated PR-10 proteins vary significantly, their other physical properties are very close.

  7. Author index

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Editor's Choice
    6. Review Articles
    7. Original Articles
    8. Author index
    9. Table of Contents
    1. You have free access to this content
      Author index (page 430)

      Article first published online: 2 JAN 2014 | DOI: 10.1111/febs.12628

  8. Table of Contents

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Editor's Choice
    6. Review Articles
    7. Original Articles
    8. Author index
    9. Table of Contents
    1. You have free access to this content
      Table of Contents (pages 431–432)

      Article first published online: 2 JAN 2014 | DOI: 10.1111/febs.12629

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